Where Microbial Genomics meets Ecology

The Amazon Forest
is the largest terrestrial ecosystem on Earth, yet the least understood
regarding its microbial diversity. The increasing demand for food,
fiber, and biofuels has caused a shift in forest to agriculture. This
is the largest land use change going on around the world and expected
to cause

ecosystem level
changes that will threaten biodiversity and
modify Earth's biogeochemical cycles.
In this research project, we ask the following questions:

(1) What are the bacterial taxa present in the Amazon rainforest soils?

(2) How are microbial communities organized in space and time in
tropical systems?

(3) What are the functional and taxonomic alterations caused by
forest-to-agriculture conversion?

A combination of high throughput sequencing of the 16S
rRNA gene,
functional genes, and cultivation of microorganisms has been used to
study the impact of land use change in microbial communities and their
ecosystem services. Our lab has been particularly interested in the
role of nitrogen fixers in maintaining a steady N supply in the forest.
This has important ecosystem consequences as effective C sequestration
depends on the N content.

2. Systems
Biology at Population Level.

Wood-feeding termites are model bioconverters,
harboring an entire microbial community orchestrated to transform
cellulose, hemicellulose and lignin into soluble oligosaccharides, H2,
and methane, among other intermediates of interest for biofuel
production. Among the many bacterial species found in the termite
hindgut, members of phylum Verrucomicrobia are always observed
in molecular surveys of the 16S rRNA gene, but rarely captured in
isolation studies. Our laboratory has maintained a small population of Verrucomicrobia
isolates
and has been using a combination of physiological studies and 'omics
tools to understand their ecological attributes and functional roles in
the termite gut. We hypothesize that intraspecies variation is as an
essential component of ecotypic differences and a stabilizing force in
ecosystem resilience. The genomes of the Termite Associated
Verrucomicrobia (TAV) strains have been sequenced, whole
genome expression profiles have been contrasted and their proteomes
measured. In addition, we are interested in identifying whole cell
regulatory networks involded in gene expression under low O2
concentration.
See the following publications:

3.
Climate Change in California dairy - forage systems.

One
of the many challenges in dairy - forage farms in California is the
generation of massive amounts of manure. The application of
animal waste to soil has been linked to increases in greenhouse gases
emissions, but the reasons remain elusive. At the heart of greenhouse
gas emissions lies microbial communities responsible for different
steps of multiple biogeochemical cycles. We aim to understand the
effects of manure fertilization on microbial communities during plant
growth.

4. Microbial and Plant Indicators of Soil Health

2018
NEWS!
Soil health is defined as the capacity for soil to function as a vital
living system to sustain biological productivity, maintain
environmental quality and promote plant, animal, and human health. Our
central hypothesis is that poor soil health resuls in the increase of
plant and microbial stresses, similar to human health metrics. Theses
stresses can be quantified as biological indicators. We will use
metagenomics to identify and quantify genes associated with
environmental stresses in agricultural intensive conditions.